Table A5.

Distances for short-sequences data set. Median of calculated distances for each reference set of the synthetic control data set (sequence length of 300 amino acids, no ASRV). Order of methods and values for k are as in Table A1.

				Reference set of ASRV data
No.	Method		k	1	2	3	4	5	6	7
1	d ML	AA	—	0.7512	1.0948	1.5985	2.0736	2.4174	2.9717	3.3904
2	d PB-ML	CE	—	1.6917	2.1449	2.6389	2.9273	3.0302	3.1279	3.1704
3	d PB-SIM	CE	—	8.1736	8.9673	9.5701	9.8498	9.9464	10.048	10.076
4	d PB-ML	AA	—	0.9011	1.2594	1.7497	2.0307	2.1513	2.2199	2.2504
5	d PB-SIM	AA	—	5.8913	7.2013	8.3587	8.8410	9.0104	9.1216	9.1536
6	d P	CE	5	0.6658	0.8564	0.9346	0.9541	0.9627	0.9695	0.9700
7	d ACS	CE	—	0.8030	0.9004	0.9506	0.9678	0.9781	0.9871	0.9892
8	d E	CE	5	531	568	582	588	590	590	592
9	d P	AA	4	0.8566	0.9553	0.9853	0.9910	0.9949	0.9953	0.9954
10	d F	CE	5	1.5378	1.8705	2.0634	2.1180	2.1465	2.1758	2.1758
11	d E	AA	4	554	580	590	592	594	594	594
13	d F	AA	4	1.7678	2.0641	2.2064	2.2374	2.2695	2.2695	2.2695
14	d ACS	AA	—	1.2130	1.3537	1.4238	1.4475	1.4597	1.4713	1.4728
15	d LZ	CE	—	0.8189	0.8548	0.8728	0.8774	0.8794	0.8819	0.8830
16	d S	CE	5	62.255	68.090	70.418	71.976	72.231	72.839	72.479
17	d LZ	AA	—	0.8366	0.8668	0.8795	0.8842	0.8861	0.8884	0.8880
19	d S	AA	4	3.2320	3.4452	3.5341	3.5909	3.5829	3.5996	3.5983
20	d C	AA	3	0.4674	0.4920	0.5044	0.5078	0.5095	0.5102	0.5105
21	d C	CE	4	0.4623	0.4888	0.5027	0.5067	0.5091	0.5097	0.5102
22	d W	AA	(1)	0.0154	0.0202	0.0245	0.0273	0.0296	0.0325	0.0334